The matrix is one of the most critical components of MALDI-TOF MS. The matrix serves several key functions in the MALDI-TOF MS process. First, it serves to coat the protein molecules and when dry, co-crystalizes and protects them from the direct deleterious effects of the laser. Second, it imparts a positively charged ion (H+ or Na+) on the proteins thus enabling their flight through the negatively charged vacuum flight tube. Third, it absorbs energy from the laser and transfers it via heat to allow desorption. Finally, it is the "charge" in the "mass to charge" ratio calculated for the spectra.

There are many matrices that can be used, and they have profound effects on the sensitivity and accuracy of the method. The most commonly used matrix in whole-cell microorganism identification is a phenolic acid compound namely, alpha-cyano-4-hydroxycinnamic acid (CHCA). Keep in mind that the matrix contains caustic components and appropriate safety measures should be in place for use. The shelf life for reconstituted matrix is seven days. Note that other matrices can be used for different applications of MALDI-TOF MS (eg, sinapic acid for mycobacteria). The matrix can be applied to either air dried or "wet" biomass spot on the target. As previously noted, the matrix must be allowed to completely evaporate after it is deposited on the specimen; the organisms are now non-viable. This allows the solvent to be removed leaving a solid, co-crystallized sample that is ready to be placed in the instrument. Once dry, our experience shows the admixture is stable for at least 8 hours prior to testing. The arrow in the image demonstrates the clumped, co-crystallized matrix as seen from the viewfinder in the Bruker Microflex™ MS system.